PDB-3no0: Aquifex aeolicus type IIA topoisomerase C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 3no0

Title

Aquifex aeolicus type IIA topoisomerase C-terminal domain

Components

DNA gyrase subunit A

Keywords

ISOMERASE / DNA topology / topoisomerase / Aquifex aeolicus / C-terminal domain / gyrase / DNA binding protein

Function / homology

Function and homology information

DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 1.3004 Å

Authors

Tretter, E.M. / Lerman, J.C. / Berger, J.M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs.
Authors: Tretter, E.M. / Lerman, J.C. / Berger, J.M.

History

Deposition	Jun 24, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	3no0_validation.pdf.gz	476.7 KB	Display	wwPDB validaton report
Full document	3no0_full_validation.pdf.gz	483.8 KB	Display
Data in XML	3no0_validation.xml.gz	42.3 KB	Display
Data in CIF	3no0_validation.cif.gz	64.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/no/3no0 ftp://data.pdbj.org/pub/pdb/validation_reports/no/3no0	HTTPS FTP

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Related structure data

Similar structure data	4u5i-2 5hos-d 4w85-2 4u3a-2 1i6n-d 2xly-d 5z44-1 4u3a-1 4a3u-2 6uba-9 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#73 - Jan 2006 Topoisomerase similarity (8) #131 - Nov 2010 Inteins similarity (6)

Deposited unit

A: DNA gyrase subunit A

B: DNA gyrase subunit A

C: DNA gyrase subunit A

hetero molecules

93.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA gyrase subunit A

hetero molecules

defined by author&software
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DNA gyrase subunit A

hetero molecules

defined by author&software
31 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: DNA gyrase subunit A

hetero molecules

defined by author&software
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.513, 49.624, 120.350
Angle α, β, γ (deg.)	91.57, 99.75, 113.48
Int Tables number	1
Space group name H-M	P1

#1: Protein	DNA gyrase subunit A Mass: 30702.777 Da / Num. of mol.: 3 / Fragment: UNP Residues 494-732 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_980, gyrA, ParC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67108, EC: 5.99.1.3
#2: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 948 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE UNP SEQUENCE FOR THIS ENTRY TERMINATES PREMATURELY DUE TO A SEQUENCE FRAME SHIFT. THE CORRECT C- ...THE UNP SEQUENCE FOR THIS ENTRY TERMINATES PREMATURELY DUE TO A SEQUENCE FRAME SHIFT. THE CORRECT C-TERMINUS SEQUENCE CONTINUES WITH DKINQKDIPLSTKKSIPRTRWKLEDDEIIKVVIKKSE

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.54	51.5
2
3
4

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
291	1	vapor diffusion, hanging drop	7.5	50 mM NaCL, 10mM Tris-HCl pH 7.5, 225 mM NH4NO3, 20% PEG 3500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291	2	vapor diffusion, hanging drop	7.5	50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10mM K2Pt(CN4), VAPOR DIFFUSION, HANGING DROP, temperature 291K
291	3	vapor diffusion, hanging drop	7.5	50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM K2PtCl4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291	4	vapor diffusion, hanging drop	7.5	50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM NaWO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1
4	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.3.1	1	1.1
SYNCHROTRON	ALS	8.3.1	2	1.071
SYNCHROTRON	ALS	8.3.1	3	1.071
SYNCHROTRON	ALS	8.3.1	4	1.214

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Apr 20, 2007
ADSC QUANTUM 315r	2	CCD	May 9, 2007
ADSC QUANTUM 315r	3	CCD	May 9, 2007
ADSC QUANTUM 315r	4	CCD	May 9, 2007

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double flat crystal, Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Double flat crystal, Si(111)	SINGLE WAVELENGTH	M	x-ray	1
3	Double flat crystal, Si(111)	SINGLE WAVELENGTH	M	x-ray	1
4	Double flat crystal, Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.1	1
2	1.071	1
3	1.214	1

Reflection

Resolution: 1.3→40.851 Å / Num. all: 222500 / Num. obs: 208073 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / B_iso Wilson estimate: 15.36 Å² / R_merge(I) obs: 0.031 / Net I/σ(I): 28.2

Reflection shell

Resolution: 1.3→1.315 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.357 / Mean I/σ(I) obs: 2.4 / Num. unique all: 18736 / % possible all: 84.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
HKL-2000		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MIRAS / Resolution: 1.3004→40.851 Å / SU ML: 0.2 / Phase error: 18.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1894	10451	5.02 %	random, 5%
R_work	0.1725	-	-	-
obs	0.1734	208073	93.51 %	-
all	-	222500	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.454 Å² / k_sol: 0.354 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4513 Å²	1.3291 Å²	0.0436 Å²
2-	-	1.8789 Å²	-1.5534 Å²
3-	-	-	-1.4276 Å²

Refinement step

Cycle: LAST / Resolution: 1.3004→40.851 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6489	0	70	948	7507

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	7249
X-RAY DIFFRACTION	f_angle_d	1.501	9882
X-RAY DIFFRACTION	f_dihedral_angle_d	15.415	2952
X-RAY DIFFRACTION	f_chiral_restr	0.089	1166
X-RAY DIFFRACTION	f_plane_restr	0.008	1248

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.3004-1.3152	0.2483	283	0.2366	5320	X-RAY DIFFRACTION	75
1.3152-1.3306	0.2573	350	0.2243	6099	X-RAY DIFFRACTION	88
1.3306-1.3469	0.2181	321	0.2064	6362	X-RAY DIFFRACTION	90
1.3469-1.3639	0.202	334	0.2079	6341	X-RAY DIFFRACTION	91
1.3639-1.3819	0.2287	332	0.2094	6454	X-RAY DIFFRACTION	91
1.3819-1.4008	0.2491	348	0.199	6446	X-RAY DIFFRACTION	91
1.4008-1.4208	0.2054	337	0.1911	6442	X-RAY DIFFRACTION	92
1.4208-1.442	0.2187	334	0.184	6475	X-RAY DIFFRACTION	92
1.442-1.4645	0.1929	361	0.1748	6505	X-RAY DIFFRACTION	92
1.4645-1.4886	0.1818	343	0.1656	6439	X-RAY DIFFRACTION	92
1.4886-1.5142	0.1972	343	0.1714	6597	X-RAY DIFFRACTION	93
1.5142-1.5418	0.1928	352	0.1711	6506	X-RAY DIFFRACTION	93
1.5418-1.5714	0.1876	359	0.1606	6560	X-RAY DIFFRACTION	93
1.5714-1.6035	0.1899	335	0.1672	6719	X-RAY DIFFRACTION	94
1.6035-1.6384	0.21	339	0.1662	6482	X-RAY DIFFRACTION	94
1.6384-1.6765	0.1853	364	0.1637	6630	X-RAY DIFFRACTION	94
1.6765-1.7184	0.1825	393	0.1589	6653	X-RAY DIFFRACTION	94
1.7184-1.7649	0.1645	352	0.1619	6684	X-RAY DIFFRACTION	95
1.7649-1.8168	0.1741	327	0.1597	6714	X-RAY DIFFRACTION	95
1.8168-1.8754	0.178	320	0.1599	6698	X-RAY DIFFRACTION	95
1.8754-1.9425	0.1788	369	0.1574	6690	X-RAY DIFFRACTION	96
1.9425-2.0202	0.1737	336	0.1543	6781	X-RAY DIFFRACTION	96
2.0202-2.1122	0.1717	374	0.154	6783	X-RAY DIFFRACTION	96
2.1122-2.2235	0.172	387	0.1574	6786	X-RAY DIFFRACTION	97
2.2235-2.3628	0.1902	352	0.164	6831	X-RAY DIFFRACTION	97
2.3628-2.5452	0.1872	328	0.1685	6893	X-RAY DIFFRACTION	97
2.5452-2.8013	0.1732	353	0.1787	6880	X-RAY DIFFRACTION	98
2.8013-3.2065	0.1812	365	0.1686	6929	X-RAY DIFFRACTION	98
3.2065-4.0393	0.1599	422	0.1498	6898	X-RAY DIFFRACTION	99
4.0393-40.8709	0.172	338	0.1514	7025	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4388	-0.1086	-0.3305	0.2688	-0.2738	1.3146	-0.1089	-0.0997	-0.0396	0.031	0.048	0.0333	0.2925	-0.0363	0.0599	0.1733	0.0104	0.0176	0.1169	0.0081	0.1168	44.1286	-9.4919	87.4761
2	0.7438	0.0886	-0.1589	0.8727	0.8652	2.1316	-0.0603	0.0431	-0.2537	0.1839	-0.0645	0.0738	0.5177	-0.1905	0.1476	0.1999	-0.0375	0.0386	0.0983	-0.0044	0.1742	43.2853	-14.3835	76.6594
3	1.4233	0.0365	-0.2037	0.8798	0.767	2.0282	-0.025	0.2282	-0.1835	-0.015	0.02	-0.0842	0.1376	0.071	-0.0053	0.1133	0.0051	0.0106	0.1256	-0.0371	0.121	49.2228	-10.526	64.9726
4	0.7077	0.0222	-0.329	1.2392	0.3041	0.5529	0.0263	0.2846	0.0406	-0.3498	0.0097	-0.0565	-0.1866	0.0071	-0.0447	0.1669	-0.0069	0.0199	0.1573	0.0016	0.101	50.7907	0.944	61.0998
5	1.4918	0.6695	-1.9444	4.0196	0.0225	2.7819	-0.3723	-0.2205	-0.3359	-0.0884	0.1976	-1.0287	-0.0805	1.7517	0.1366	0.1327	-0.0608	0.0845	0.4327	-0.0503	0.3446	65.4593	2.7522	65.5712
6	0.6217	-0.2108	0.0308	1.1908	0.3227	1.0211	-0.0066	0.0583	0.1352	-0.1387	0.0475	-0.1476	-0.3716	0.0317	-0.0195	0.1873	-0.0166	0.0145	0.1018	0.0307	0.1332	50.7034	10.8784	69.8063
7	0.4948	0.0278	-0.3379	0.5665	0.5207	1.436	0.0294	-0.042	0.0954	0.0428	0.0433	-0.0873	-0.3489	-0.0015	-0.0636	0.1807	0.0075	0.0006	0.0824	0.0203	0.1408	47.1645	11.837	80.9066
8	0.2114	0.4464	-0.408	1.0341	-0.3214	1.52	0.0106	0.0046	-0.011	0.0839	0.0095	-0.1624	-0.1535	0.1957	0.0023	0.1412	0.0012	-0.0305	0.1153	0.0119	0.1433	48.3447	6.5193	83.0549
9	0.5926	-0.1726	-0.5748	0.4049	0.8712	1.6943	0.1274	-0.0786	0.0551	0.0175	0.0871	-0.0682	-0.1337	0.1031	-0.1496	0.1367	-0.0159	0.0158	0.1771	-0.0389	0.1182	38.079	29.0406	47.4184
10	0.6479	-0.0778	-0.4789	1.6168	0.9832	0.8102	0.0573	-0.0887	0.0055	0.0183	-0.1437	0.0441	-0.042	-0.1994	0.0926	0.1128	-0.0001	-0.0039	0.2238	-0.0247	0.0969	29.714	21.4826	44.9508
11	0.6053	0.3825	-0.0563	0.7931	0.6133	1.2171	0.055	0.0059	-0.1642	0.0401	-0.1238	0.0407	0.0781	-0.2378	0.0593	0.0753	-0.0321	-0.0175	0.1486	-0.0088	0.1075	30.7784	9.8617	37.9678
12	1.2413	0.1208	-0.2595	0.3022	0.3525	1.349	0.0102	0.3016	-0.2338	-0.0513	-0.0753	0.0185	0.0872	-0.0855	0.0455	0.1192	-0.0022	-0.0256	0.1862	-0.0661	0.1627	36.4218	7.7962	27.2699
13	5.414	1.4413	2.1919	0.5321	1.1025	3.2525	0.2638	0.2453	-1.0648	0.5286	0.0028	-0.3548	0.5621	0.452	-0.3533	0.269	0.0917	-0.0879	0.1981	-0.0247	0.3277	49.3526	0.9462	33.6705
14	0.8862	0.0885	-0.6184	0.4663	0.244	1.2862	0.0572	0.2342	-0.0504	-0.0838	0.0419	-0.0861	-0.1119	0.1161	-0.1002	0.1085	0.0079	-0.0051	0.2232	-0.0387	0.1038	46.7981	15.5347	24.2835
15	0.7628	-0.0636	-0.5707	0.4224	0.4728	1.4744	0.1278	-0.0857	0.1475	-0.0657	0.154	-0.1962	-0.1667	0.3165	-0.2064	0.1349	-0.0476	0.0505	0.2048	-0.0387	0.1341	50.707	26.1061	28.5689
16	1.6455	-0.4508	-1.3237	0.7378	0.8386	1.398	0.196	-0.0845	0.0057	-0.1144	0.0314	-0.0981	-0.1077	0.2135	-0.2064	0.1124	-0.0328	0.019	0.187	-0.0323	0.1319	49.5733	25.0943	35.1295
17	0.8869	-0.3263	-0.6462	0.5896	-0.1388	1.5396	0.0946	0.1087	-0.0333	-0.0225	-0.0057	0.021	-0.0955	-0.1206	-0.0799	0.104	0.0017	0	0.0822	0.0109	0.1015	57.3577	14.8657	-21.6275
18	1.6899	-0.3281	-0.9163	0.3693	-0.2069	2.1135	0.0724	0.1774	0.0772	-0.0466	0.0035	0.0381	-0.1278	-0.257	-0.0666	0.0817	0.0121	-0.018	0.0711	0.0294	0.1022	48.7139	16.1983	-13.3325
19	0.768	-0.2169	-0.1728	0.3437	-0.3233	1.0325	-0.0008	-0.1212	0.0359	0.0335	0.0131	0.0678	-0.0392	-0.0687	-0.0177	0.0879	-0.0051	0.0076	0.0763	-0.0008	0.1178	49.4126	15.1478	-0.0982
20	0.6206	-0.4678	0.2458	0.6024	-0.2506	0.6491	-0.0691	-0.1909	-0.0502	0.0562	0.0727	0.0591	0.0019	-0.0456	-0.0108	0.0996	-0.0069	0.0121	0.1105	0.0193	0.1029	55.6508	6.5151	6.3895
21	7.4344	4.594	1.3091	4.2807	2.0675	1.3907	0.1441	-0.7764	0.2526	0.2166	-0.0288	-0.1741	-0.26	0.4569	-0.0997	0.1492	-0.0269	-0.0282	0.2183	-0.0598	0.1567	68.1695	14.9096	9.7294
22	0.7475	-0.37	-0.0363	0.3308	-0.2508	0.4557	-0.0358	-0.0739	-0.0748	-0.045	-0.0002	0.0026	0.0968	0.0776	0.0367	0.0628	-0.0046	0.0038	0.0482	0.0302	0.0791	65.915	0.2502	0.5001
23	0.6711	-0.5362	0.5263	1.3153	-0.6326	0.8656	0.0508	0.0834	-0.0075	-0.1501	-0.0845	0.0147	0.1758	0.1447	0.0187	0.1008	0.0164	0.0208	0.0631	0.0283	0.0863	70.047	-0.7052	-10.823
24	1.3626	-1.2971	0.9228	1.4242	-1.1754	1.5155	0.0431	0.0944	0.0529	-0.0578	-0.1291	-0.0157	0.1275	0.1507	0.0739	0.0741	0.0024	0.0086	0.0603	0.0206	0.0834	67.827	4.9396	-12.7029

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND RESSEQ 494:523	A	494 - 523
2	X-RAY DIFFRACTION	2	CHAIN A AND RESSEQ 524:574	A	524 - 574
3	X-RAY DIFFRACTION	3	CHAIN A AND RESSEQ 575:617	A	575 - 617
4	X-RAY DIFFRACTION	4	CHAIN A AND RESSEQ 618:653	A	618 - 653
5	X-RAY DIFFRACTION	5	CHAIN A AND RESSEQ 654:660	A	654 - 660
6	X-RAY DIFFRACTION	6	CHAIN A AND RESSEQ 661:718	A	661 - 718
7	X-RAY DIFFRACTION	7	CHAIN A AND RESSEQ 719:750	A	719 - 750
8	X-RAY DIFFRACTION	8	CHAIN A AND RESSEQ 751:769	A	751 - 769
9	X-RAY DIFFRACTION	9	CHAIN B AND RESSEQ 492:523	B	492 - 523
10	X-RAY DIFFRACTION	10	CHAIN B AND RESSEQ 524:574	B	524 - 574
11	X-RAY DIFFRACTION	11	CHAIN B AND RESSEQ 575:617	B	575 - 617
12	X-RAY DIFFRACTION	12	CHAIN B AND RESSEQ 618:653	B	618 - 653
13	X-RAY DIFFRACTION	13	CHAIN B AND RESSEQ 654:660	B	654 - 660
14	X-RAY DIFFRACTION	14	CHAIN B AND RESSEQ 661:718	B	661 - 718
15	X-RAY DIFFRACTION	15	CHAIN B AND RESSEQ 719:750	B	719 - 750
16	X-RAY DIFFRACTION	16	CHAIN B AND RESSEQ 751:769	B	751 - 769
17	X-RAY DIFFRACTION	17	CHAIN C AND RESSEQ 494:523	C	494 - 523
18	X-RAY DIFFRACTION	18	CHAIN C AND RESSEQ 524:574	C	524 - 574
19	X-RAY DIFFRACTION	19	CHAIN C AND RESSEQ 575:617	C	575 - 617
20	X-RAY DIFFRACTION	20	CHAIN C AND RESSEQ 618:653	C	618 - 653
21	X-RAY DIFFRACTION	21	CHAIN C AND RESSEQ 654:660	C	654 - 660
22	X-RAY DIFFRACTION	22	CHAIN C AND RESSEQ 661:718	C	661 - 718
23	X-RAY DIFFRACTION	23	CHAIN C AND RESSEQ 719:750	C	719 - 750
24	X-RAY DIFFRACTION	24	CHAIN C AND RESSEQ 751:769	C	751 - 769

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